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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
add() (RvapiMetadata method)
add_array_to_mtz_dataset() (ExperimentalData method)
add_console() (LogController method)
,
[1]
add_logfile() (LogController method)
,
[1]
adjust_paths_of_files() (SimbadOutput method)
ALPHA (AmoreRotationScore attribute)
alt (LatticeSearchResult attribute)
AmoreRotationScore (class in simbad.core.amore_score)
AmoreRotationSearch (class in simbad.rotsearch.amore_search)
AmoreRotsearchParser (class in simbad.parsers.rotsearch_parser)
angle_penalty (LatticeSearchResult attribute)
anode() (AnodeSearch method)
AnodeParser (class in simbad.parsers.anode_parser)
AnodeSearch (class in simbad.mr.anomalous_util)
AnomScore (class in simbad.core.anode_score)
autohigh (Phaser attribute)
B
BETA (AmoreRotationScore attribute)
C
calculate_content_ncopies_from_file() (MatthewsProbability method)
calculate_content_ncopies_from_struct() (MatthewsProbability method)
calculate_from_file() (SolventContent method)
calculate_from_struct() (SolventContent method)
calculate_niggli_cell() (LatticeSearch static method)
calculate_penalty() (simbad.lattice.lattice_search.LatticeSearch class method)
calculate_probability() (simbad.lattice.lattice_search.LatticeSearch class method)
calculate_volume_difference() (simbad.lattice.lattice_search.LatticeSearch class method)
CC_F (AmoreRotationScore attribute)
CC_F_Z_score (AmoreRotationScore attribute)
CC_I (AmoreRotationScore attribute)
CC_P (AmoreRotationScore attribute)
CC_P_Z_score (AmoreRotationScore attribute)
CCP4 (class in simbad.command_line)
,
[1]
CCP4RootDirectory (class in simbad.command_line)
,
[1]
CCP4Version (class in simbad.command_line)
,
[1]
cell_parameters (MrSubmit attribute)
,
[1]
cell_within_tolerance() (simbad.lattice.lattice_search.LatticeSearch class method)
change_space_group() (ExperimentalData method)
check_anomalous_arrays() (ExperimentalData static method)
check_contrast() (in module simbad.mr.molrep_mr)
check_sg() (LatticeSearch static method)
cleanup() (AnodeSearch method)
(in module simbad.command_line)
,
[1]
close() (LogController method)
,
[1]
contaminant_argparse() (in module simbad.command_line.simbad_contaminant)
ContaminantSearchResult (class in simbad.command_line.simbad_database)
convert_dat_to_pdb() (in module simbad.db)
convert_pdb_to_dat() (in module simbad.db)
copy_results() (LatticeSearch method)
create_amplitude_array() (ExperimentalData method)
create_anomalous_amplitude_array() (ExperimentalData method)
create_anomalous_intensity_array() (ExperimentalData method)
create_contaminant_db() (in module simbad.command_line.simbad_database)
create_contaminant_results_tab() (SimbadOutput method)
create_db_argparse() (in module simbad.command_line.simbad_database)
create_db_custom() (in module simbad.command_line.simbad_database)
create_graphs() (SimbadOutput static method)
create_lattice_db() (in module simbad.command_line.simbad_database)
create_lattice_results_tab() (SimbadOutput method)
create_log_tab() (SimbadOutput method)
create_merged_intensity_array() (ExperimentalData method)
create_morda_db() (in module simbad.command_line.simbad_database)
create_morda_db_results_tab() (SimbadOutput method)
create_reconstructed_amplitude_array() (ExperimentalData method)
create_table() (SimbadOutput method)
CRITICAL (LogColors attribute)
,
[1]
crystal_data() (in module simbad.util.mtz_util)
D
dano_peak_height (AnomScore attribute)
(MrScore attribute)
dat_path (AmoreRotationScore attribute)
(DatModelScore attribute)
(PhaserRotationScore attribute)
DatModelScore (class in simbad.core.dat_score)
DEBUG (LogColors attribute)
,
[1]
(LogLevels attribute)
,
[1]
DEFAULT (LogColors attribute)
,
[1]
display_results() (SimbadOutput method)
display_summary_tab() (SimbadOutput method)
download_morda() (in module simbad.command_line.simbad_database)
download_results() (LatticeSearch method)
E
ERROR (LogColors attribute)
,
[1]
(LogLevels attribute)
,
[1]
evaluate_results() (Molrep method)
exit_error() (in module simbad.exit)
ExperimentalData (class in simbad.util.mtz_util)
F
f (MrSubmit attribute)
,
[1]
(Phaser attribute)
,
[1]
fft() (MrSubmit static method)
,
[1]
FileCollection (class in simbad.util.simbad_results)
final_r_fact (MrScore attribute)
final_r_free (MrScore attribute)
find_simbad_dat_files() (in module simbad.db)
fix_path() (SimbadOutput method)
format() (LogColorFormatter method)
,
[1]
free (MrSubmit attribute)
,
[1]
from_file() (PdbStructure method)
from_pdb_code() (PdbStructure method)
G
GAMMA (AmoreRotationScore attribute)
get_array_types() (ExperimentalData method)
get_chunk_size() (in module simbad.rotsearch)
,
[1]
get_files() (SimbadResults method)
get_labels() (in module simbad.util.mtz_util)
get_levelname() (LogController method)
,
[1]
get_logger() (LogController method)
,
[1]
get_mtz_info() (MrSubmit method)
,
[1]
get_pdb_content() (PdbStructure static method)
get_total_chunk_cycles() (in module simbad.rotsearch)
,
[1]
get_work_dir() (in module simbad.command_line)
,
[1]
H
hires (Phaser attribute)
,
[1]
hklin (Molrep attribute)
(Phaser attribute)
,
[1]
(Refmac attribute)
hklout (Refmac attribute)
I
i (MrSubmit attribute)
,
[1]
(Phaser attribute)
,
[1]
Icp (AmoreRotationScore attribute)
INFO (LogLevels attribute)
,
[1]
init_from_ccp4i2_xml() (SimbadOutput method)
integration_box (PdbStructure attribute)
intrad (DatModelScore attribute)
is_valid_dat() (in module simbad.db)
is_valid_db_location() (in module simbad.command_line.simbad_database)
is_valid_dir() (in module simbad.command_line)
,
[1]
is_valid_file() (in module simbad.command_line)
,
[1]
K
keep_first_chain_only() (PdbStructure method)
L
lattice_argparse() (in module simbad.command_line.simbad_lattice)
lattice_db_fname (LatticeSearch attribute)
LatticeSearch (class in simbad.lattice.lattice_search)
LatticeSearchResult (class in simbad.core.lattice_score)
leave_timestamp() (in module simbad.command_line.simbad_database)
length_penalty (LatticeSearchResult attribute)
level_valid() (LogController static method)
,
[1]
llg (PhaserRotationScore attribute)
LogColorFormatter (class in simbad.command_line)
,
[1]
LogColors (class in simbad.command_line)
,
[1]
LogController (class in simbad.command_line)
,
[1]
logfile (Molrep attribute)
(Phaser attribute)
,
[1]
(Refmac attribute)
LogLevels (class in simbad.command_line)
,
[1]
M
main() (in module simbad.command_line.simbad_contaminant)
(in module simbad.command_line.simbad_database)
(in module simbad.command_line.simbad_full)
(in module simbad.command_line.simbad_lattice)
(in module simbad.command_line.simbad_main)
(in module simbad.command_line.simbad_morda)
make_output_dir() (in module simbad.command_line)
,
[1]
make_workdir() (in module simbad.command_line)
,
[1]
MatthewsProbability (class in simbad.util.matthews_prob)
model_dir (LatticeSearch attribute)
molecular_weight (PdbStructure attribute)
Molrep (class in simbad.mr.molrep_mr)
molrep() (Molrep static method)
molrep_score (MrScore attribute)
molrep_tfscore (MrScore attribute)
MolrepParser (class in simbad.parsers.molrep_parser)
morda_argparse() (in module simbad.command_line.simbad_morda)
mr_job_succeeded() (in module simbad.rotsearch)
,
[1]
mr_program (AnodeSearch attribute)
(MrSubmit attribute)
,
[1]
mr_python_module (MrSubmit attribute)
,
[1]
mr_succeeded_csvfile() (in module simbad.mr)
,
[1]
mr_succeeded_log() (in module simbad.mr)
,
[1]
MrScore (class in simbad.core.mr_score)
MrSubmit (class in simbad.mr)
,
[1]
mtz (AnodeSearch attribute)
(MrSubmit attribute)
,
[1]
mtz2sca() (AnodeSearch method)
mw_diff (DatModelScore attribute)
N
n_results (RvapiMetadata attribute)
nchains (PdbStructure attribute)
nearest_atom (AnomScore attribute)
(MrScore attribute)
nmol (DatModelScore attribute)
(Molrep attribute)
(Phaser attribute)
,
[1]
no_stdout() (in module simbad.util.matthews_prob)
NOTSET (LogLevels attribute)
,
[1]
nres (PdbStructure attribute)
Number_of_rotation_searches_producing_peak (AmoreRotationScore attribute)
O
output_dir (AnodeSearch attribute)
(MrSubmit attribute)
,
[1]
output_files() (in module simbad.util)
,
[1]
output_log_files() (SimbadOutput method)
output_mtz() (ExperimentalData method)
output_result_files() (SimbadOutput method)
P
pdb_code (AmoreRotationScore attribute)
(ContaminantSearchResult attribute)
(DatModelScore attribute)
(LatticeSearchResult attribute)
(MrScore attribute)
(PhaserRotationScore attribute)
pdb_in_results() (LatticeSearch static method)
pdb_path (LatticeSearchResult attribute)
pdbin (Molrep attribute)
(Phaser attribute)
,
[1]
(Refmac attribute)
pdbout (Molrep attribute)
(Phaser attribute)
(Refmac attribute)
PdbStructure (class in simbad.util.pdb_util)
Phaser (class in simbad.mr.phaser_mr)
(class in simbad.rotsearch.phaser_rotation_search)
phaser_llg (MrScore attribute)
phaser_rfz (MrScore attribute)
phaser_tfz (MrScore attribute)
PhaserParser (class in simbad.parsers.phaser_parser)
PhaserRotationScore (class in simbad.core.phaser_score)
PhaserRotationSearch (class in simbad.rotsearch.phaser_search)
PhaserRotsearchParser (class in simbad.parsers.rotsearch_parser)
print_header() (in module simbad.command_line)
,
[1]
probability_score (LatticeSearchResult attribute)
process_miller_arrays() (ExperimentalData method)
R
read_dat() (in module simbad.db)
refine_cycles (MrSubmit attribute)
,
[1]
refine_program (MrSubmit attribute)
,
[1]
refine_python_module (MrSubmit attribute)
,
[1]
refine_type (MrSubmit attribute)
,
[1]
Refmac (class in simbad.mr.refmac_refine)
refmac() (Refmac static method)
RefmacParser (class in simbad.parsers.refmac_parser)
rel_path_for_jscofe() (SimbadOutput method)
reset() (LogController method)
,
[1]
resolution (MrSubmit attribute)
,
[1]
result_by_score_from_csv() (in module simbad.util)
,
[1]
RF_F (AmoreRotationScore attribute)
rfz (PhaserRotationScore attribute)
rot_succeeded_log() (AmoreRotationSearch method)
(PhaserRotationSearch method)
rotation_search_factory() (in module simbad.rotsearch)
,
[1]
rotfun_stdin_template (AmoreRotationSearch attribute)
run() (AmoreRotationSearch method)
(AnodeSearch method)
(Molrep method)
(Phaser method)
,
[1]
(PhaserRotationSearch method)
(Refmac method)
RvapiMetadata (class in simbad.util.pyrvapi_results)
S
save() (PdbStructure method)
save_document() (SimbadOutput method)
ScoreBase (class in simbad.core)
,
[1]
search() (LatticeSearch method)
search_results (AmoreRotationSearch attribute)
(MrSubmit attribute)
,
[1]
(PhaserRotationSearch attribute)
search_results() (AnodeSearch method)
select_chain_by_id() (PdbStructure method)
select_chain_by_idx() (PdbStructure method)
set_crystal_symmetry() (PdbStructure method)
sgalternative (Molrep attribute)
(MrSubmit attribute)
,
[1]
(Phaser attribute)
shelxc() (AnodeSearch method)
sigf (MrSubmit attribute)
,
[1]
(Phaser attribute)
,
[1]
sigi (MrSubmit attribute)
,
[1]
(Phaser attribute)
,
[1]
simbad (module)
simbad.chemistry (module)
simbad.command_line (module)
,
[1]
simbad.command_line.simbad_contaminant (module)
simbad.command_line.simbad_database (module)
simbad.command_line.simbad_full (module)
simbad.command_line.simbad_lattice (module)
simbad.command_line.simbad_main (module)
simbad.command_line.simbad_morda (module)
simbad.core (module)
,
[1]
simbad.core.amore_score (module)
simbad.core.anode_score (module)
simbad.core.dat_score (module)
simbad.core.lattice_score (module)
simbad.core.mr_score (module)
simbad.core.phaser_score (module)
simbad.db (module)
simbad.exit (module)
simbad.lattice (module)
,
[1]
simbad.lattice.lattice_search (module)
simbad.mr (module)
,
[1]
simbad.mr.anomalous_util (module)
simbad.mr.molrep_mr (module)
simbad.mr.phaser_mr (module)
simbad.mr.refmac_refine (module)
simbad.parsers (module)
simbad.parsers.anode_parser (module)
simbad.parsers.molrep_parser (module)
simbad.parsers.phaser_parser (module)
simbad.parsers.refmac_parser (module)
simbad.parsers.rotsearch_parser (module)
simbad.rotsearch (module)
,
[1]
simbad.rotsearch.amore_search (module)
simbad.rotsearch.phaser_rotation_search (module)
simbad.rotsearch.phaser_search (module)
simbad.util (module)
,
[1]
simbad.util.matthews_prob (module)
simbad.util.mtz_util (module)
simbad.util.pdb_util (module)
simbad.util.pyrvapi_results (module)
simbad.util.simbad_results (module)
simbad.version (module)
simbad_argparse() (in module simbad.command_line.simbad_full)
(in module simbad.command_line.simbad_main)
SimbadOutput (class in simbad.util.pyrvapi_results)
SimbadResults (class in simbad.util.simbad_results)
solvent (DatModelScore attribute)
(Phaser attribute)
,
[1]
SolventContent (class in simbad.util.matthews_prob)
sortfun_stdin_template (AmoreRotationSearch attribute)
space_group (ContaminantSearchResult attribute)
(Molrep attribute)
(MrSubmit attribute)
,
[1]
standardize() (PdbStructure method)
store_entry_in_rvapi_meta() (SimbadOutput method)
submit_chunk() (in module simbad.rotsearch)
,
[1]
submit_jobs() (MrSubmit method)
,
[1]
submit_mr_jobs() (in module simbad.command_line)
,
[1]
summarize() (AmoreRotationSearch method)
(LatticeSearch method)
(MrSubmit method)
,
[1]
(PhaserRotationSearch method)
summarize_result() (in module simbad.util)
,
[1]
T
tabfun_stdin_template (AmoreRotationSearch attribute)
timeout (MrSubmit attribute)
,
[1]
(Phaser attribute)
,
[1]
to_json() (RvapiMetadata method)
top_files() (SimbadResults method)
total_penalty (LatticeSearchResult attribute)
U
uniprot_mnemonic (ContaminantSearchResult attribute)
uniprot_name (ContaminantSearchResult attribute)
unit_cell (LatticeSearchResult attribute)
V
validate_compressed_database() (in module simbad.command_line.simbad_database)
volume_difference (LatticeSearchResult attribute)
W
WARNING (LogColors attribute)
,
[1]
(LogLevels attribute)
,
[1]
work_dir (Molrep attribute)
(Refmac attribute)
X
x (DatModelScore attribute)
Y
y (DatModelScore attribute)
Z
z (DatModelScore attribute)